The FAO recently estimated that demand for food would increase by 70% by 2050. The challenge will not only be on increasing the food supply, but also on improving its nutritional value. Until now, despite the call for an increased use of underutilized crops to diversify alimentation and provide sustainable agriculture, those crops remain a largely untapped reservoir of agrobiodiversity. Are they really crops for the future? In this regard, fonio (Digitaria exilis Stapf) appears as a promising crop. It is an indigenous staple cereal from Western Africa regarded as a valuable source of income, especially for small-scale farmers. It plays a crucial role in food and nutrition security: short length cycles varieties can be harvested during the shortage season. Nevertheless, fonio remains largely under-studied compared to other African cereals such as sorghum or millet. The need to characterize its genetic resources and adaptive potential to the fast-evolving environmental pressures is therefore crucial. Herein, we assess the genetic diversity of fonio and its evolutionary history at both regional and local scale. We show that genetic diversity is highly linked to geographic origin, ethnic groups and climate conditions. We discuss the implication in terms of domestication history and conservation.